HEADER ZINC ENDOPEPTIDASE 09-MAY-94 1IAA TITLE CRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC PROPERTIES TITLE 2 OF COBALT(II), COPPER(II), NICKEL(II), AND MERCURY(II) DERIVATIVES OF TITLE 3 THE ZINC ENDOPEPTIDASE ASTACIN. A CORRELATION OF STRUCTURE AND TITLE 4 PROTEOLYTIC ACTIVITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASTACIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.24.21; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASTACUS ASTACUS; SOURCE 3 ORGANISM_COMMON: BROAD-FINGERED CRAYFISH; SOURCE 4 ORGANISM_TAXID: 6715 KEYWDS ZINC ENDOPEPTIDASE EXPDTA X-RAY DIFFRACTION AUTHOR F.-X.GOMIS-RUETH,W.STOECKER,W.BODE REVDAT 4 05-JUN-24 1IAA 1 REMARK LINK REVDAT 3 24-FEB-09 1IAA 1 VERSN REVDAT 2 01-APR-03 1IAA 1 JRNL REVDAT 1 31-AUG-94 1IAA 0 JRNL AUTH F.X.GOMIS-RUTH,F.GRAMS,I.YIALLOUROS,H.NAR,U.KUSTHARDT, JRNL AUTH 2 R.ZWILLING,W.BODE,W.STOCKER JRNL TITL CRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC JRNL TITL 2 PROPERTIES OF COBALT(II), COPPER(II), NICKEL(II), AND JRNL TITL 3 MERCURY(II) DERIVATIVES OF THE ZINC ENDOPEPTIDASE ASTACIN. A JRNL TITL 4 CORRELATION OF STRUCTURE AND PROTEOLYTIC ACTIVITY. JRNL REF J.BIOL.CHEM. V. 269 17111 1994 JRNL REFN ISSN 0021-9258 JRNL PMID 8006015 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.BODE,F.-X.GOMIS-RUETH,W.STOECKER REMARK 1 TITL ASTACINS, SERRALYSINS, SNAKE VENOM AND MATRIX REMARK 1 TITL 2 METALLOPROTEINASES EXHIBIT IDENTICAL ZINC-BINDING REMARK 1 TITL 3 ENVIRONMENTS (HEXXHXXGXXH AND MET-TURN) AND TOPOLOGIES AND REMARK 1 TITL 4 SHOULD BE GROUPED INTO A COMMON FAMILY, THE 'METZINCINS' REMARK 1 REF FEBS LETT. V. 331 134 1993 REMARK 1 REFN ISSN 0014-5793 REMARK 1 REFERENCE 2 REMARK 1 AUTH W.BODE,F.X.GOMIS-RUETH,R.HUBER,R.ZWILLING,W.STOECKER REMARK 1 TITL STRUCTURE OF ASTACIN AND IMPLICATIONS FOR ACTIVATION OF REMARK 1 TITL 2 ASTACINS AND ZINC-LIGATION OF COLLAGENASES REMARK 1 REF NATURE V. 358 164 1992 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1591 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 178 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 2.133 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IAA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174081. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.88333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 65.76667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 65.76667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.88333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 LEU A 200 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 TYR A 8 CB CG CD1 CD2 CE1 CE2 CZ REMARK 480 TYR A 8 OH REMARK 480 ASN A 169 CB CG OD1 ND2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 49 -74.98 -111.61 REMARK 500 SER A 72 148.14 74.00 REMARK 500 VAL A 160 -54.66 -124.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 999 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 92 NE2 REMARK 620 2 HIS A 96 NE2 90.9 REMARK 620 3 HIS A 102 NE2 116.5 91.1 REMARK 620 4 TYR A 149 OH 96.0 172.8 87.3 REMARK 620 5 HOH A 300 O 106.1 93.2 137.2 83.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 999 DBREF 1IAA A 1 200 UNP P07584 ASTA_ASTFL 50 249 SEQRES 1 A 200 ALA ALA ILE LEU GLY ASP GLU TYR LEU TRP SER GLY GLY SEQRES 2 A 200 VAL ILE PRO TYR THR PHE ALA GLY VAL SER GLY ALA ASP SEQRES 3 A 200 GLN SER ALA ILE LEU SER GLY MET GLN GLU LEU GLU GLU SEQRES 4 A 200 LYS THR CYS ILE ARG PHE VAL PRO ARG THR THR GLU SER SEQRES 5 A 200 ASP TYR VAL GLU ILE PHE THR SER GLY SER GLY CYS TRP SEQRES 6 A 200 SER TYR VAL GLY ARG ILE SER GLY ALA GLN GLN VAL SER SEQRES 7 A 200 LEU GLN ALA ASN GLY CYS VAL TYR HIS GLY THR ILE ILE SEQRES 8 A 200 HIS GLU LEU MET HIS ALA ILE GLY PHE TYR HIS GLU HIS SEQRES 9 A 200 THR ARG MET ASP ARG ASP ASN TYR VAL THR ILE ASN TYR SEQRES 10 A 200 GLN ASN VAL ASP PRO SER MET THR SER ASN PHE ASP ILE SEQRES 11 A 200 ASP THR TYR SER ARG TYR VAL GLY GLU ASP TYR GLN TYR SEQRES 12 A 200 TYR SER ILE MET HIS TYR GLY LYS TYR SER PHE SER ILE SEQRES 13 A 200 GLN TRP GLY VAL LEU GLU THR ILE VAL PRO LEU GLN ASN SEQRES 14 A 200 GLY ILE ASP LEU THR ASP PRO TYR ASP LYS ALA HIS MET SEQRES 15 A 200 LEU GLN THR ASP ALA ASN GLN ILE ASN ASN LEU TYR THR SEQRES 16 A 200 ASN GLU CYS SER LEU HET CU A 999 1 HETNAM CU COPPER (II) ION FORMUL 2 CU CU 2+ FORMUL 3 HOH *178(H2 O) HELIX 1 1 GLY A 5 LEU A 9 5 5 HELIX 2 2 TRP A 10 GLY A 12 5 3 HELIX 3 3 SER A 23 THR A 41 1 19 HELIX 4 4 TYR A 86 GLY A 99 1 14 HELIX 5 5 HIS A 102 ARG A 106 5 5 HELIX 6 6 ASP A 108 ASN A 111 5 4 HELIX 7 7 TYR A 117 ASN A 119 5 3 HELIX 8 8 MET A 124 ASP A 129 5 6 HELIX 9 9 ASP A 175 LYS A 179 5 5 HELIX 10 10 LEU A 183 TYR A 194 1 12 SHEET 1 A 2 ALA A 2 ILE A 3 0 SHEET 2 A 2 SER A 134 ARG A 135 -1 O ARG A 135 N ALA A 2 SHEET 1 B 5 ARG A 44 PRO A 47 0 SHEET 2 B 5 VAL A 14 ALA A 20 1 N ILE A 15 O ARG A 44 SHEET 3 B 5 TYR A 54 PHE A 58 1 N VAL A 55 O PRO A 16 SHEET 4 B 5 ALA A 74 LEU A 79 1 O GLN A 75 N GLU A 56 SHEET 5 B 5 CYS A 64 SER A 66 -1 N TRP A 65 O SER A 78 SHEET 1 C 2 VAL A 113 ILE A 115 0 SHEET 2 C 2 ILE A 164 PRO A 166 -1 N VAL A 165 O THR A 114 SSBOND 1 CYS A 42 CYS A 198 1555 1555 2.04 SSBOND 2 CYS A 64 CYS A 84 1555 1555 2.03 LINK NE2 HIS A 92 CU CU A 999 1555 1555 2.03 LINK NE2 HIS A 96 CU CU A 999 1555 1555 2.07 LINK NE2 HIS A 102 CU CU A 999 1555 1555 2.05 LINK OH TYR A 149 CU CU A 999 1555 1555 2.10 LINK O HOH A 300 CU CU A 999 1555 1555 2.25 SITE 1 AC1 5 HIS A 92 HIS A 96 HIS A 102 TYR A 149 SITE 2 AC1 5 HOH A 300 CRYST1 62.000 62.000 98.650 90.00 90.00 120.00 P 31 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016129 0.009312 0.000000 0.00000 SCALE2 0.000000 0.018624 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010137 0.00000